I can't tell you with certainty, but it isn't unusual to find different spellings of Anglecised placenames. When they were first Anglicised it may have been the case that people used different spellings simply because they weren't able to spell this made up nonsense which came from Irish words which actually meant something. Of course, given that it would have been a long time ago, many people weren't literate at all in any language.
Besides this, names often change over time - misspellings that become popular...fashion...whatever. You'll see the same with the way people change the spelling of their surnames.
In my own area (north Dublin) I know of two places that have variant spellings although in both cases one spelling has taken over from the older version: Artaine has become Artane and Kinsaley has become Kinsealy (although some people still use the old version, particularly the pronounciation). There are calls for Gormonston to be respelt Gormonstown since almost everybody says it that way.
So both spellings of Clohanbeg are probably ok. The current spelling according to
www.logainm.ie is Cloghaunbeg (a third spelling!) unless there is more than one place with the same original Irish-language name in Clare - which is entirely possible.